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Problem with upgrading AcePerl

Keith Bradnam keith at thale.nott.ac.uk
Tue Dec 7 11:52:21 EST 1999


Hello,

I've just started experiencing difficulties with our AceBrowser interface
to our Arabidopsis database (AGR).  The only thing I can imagine that this
is related to is the upgraded version of AcePerl that I installed last
week.  I am new to Ace-related things and have been working through
various help files all day to no avail.  Can anyone help please?


A brief outline of problem...

When you use AceBrowser to try and retrieve a sequence object from AGR,
the following message appears in the main part of the AceBrowswer display:

" Software error:
  Can't locate auto/Ace/Object/cDNA.al in @INC (@INC contains:
  /usr/local/lib/perl5/sun4-solaris/5.00404 /usr/local/lib/perl5
  /usr/local/lib/perl5/site_perl/sun4-solaris
  /usr/local/lib/perl5/site_perl
  . /crick/web/ /crick/web/lib/perl) at
  /crick/web/apache_perl/ace/AGR-sequence line 109 "

This problem only occurs with AGR, other databases that we host (e.g.
BrassicaDB) do not have this problem.  I suspect that this is due to the
fact that AGR is the only database we host which has it's display
configured differently in SiteDefs.pm, e.g.

%DATABASES = (
              'AGR' => {
                        host       => '128.243.116.29', 
			...snipped...
                        url_mapper => \&agr_mapper,          
                        displays   => \%agr_displays,          
                       },

...snipped...

%agr_displays =
  (
   Sequence  => [ 
                 { 'url'   => 'AGR-sequence',  
                   'label' => 'Sequence Report', 
                   'icon'  => '/icons/layout.gif' },
                ],

  );



Other databases that we mirror just have 'undef' in their displays field.

We had AcePerl 1.51 and I upgraded last week to 1.57.  Nothing unusual
happened during installation, and it was only today I noticed the problem
with retrieving sequences.  We currently have AceBrowser 2.02, Apache
1.33, and Perl 5.004_04 all running on Solaris 2.6.

I've noticed that a lot of perl scripts that contain 'use Ace' often have
a version number as well, e.g. 'use Ace 1.41' - should these always point
to the latest version number?

The file which the error message relates to (auto/Ace/Object/cDNA.al) does
not seem to exist anywhere on our system, and I've still not been able to
find any script that mentions this file.

Any ideas???  To see this error in action, have a look at:

http://synteny.nott.ac.uk/perl/ace/AGR-sequence/AGR?name=EMBL%3AA47152

Hope someone can help,

Keith


~  Keith Bradnam - Developer, Arabidopsis Genome Resource (AGR)
~  Nottingham Arabidopsis Stock Centre - http://nasc.nott.ac.uk/
~  University Park, University of Nottingham, NG7 2RD, UK
~  Tel: (0115) 951 3091 






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